坏掉的maker

【提示】本文写作命令为：abysw blog 坏掉的maker

或因转移目录，maker产生了报错：

Possible precedence issue with control flow operator at /xulab/pipeline/app/miniconda3/envs/maker/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

MAKER version 2.31.11

原因描述很简单，就是说perl的东西坏了。

The problem is the bioperl or even perl installation —> “Possible precedence issue with control flow operator at /apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.”

You may have a custom install of perl without BerkleyDB setup, or need to update BioPerl. If you installed MAKER with MiniConda, then it tried to setup a custom perl and BioPerl that is broken. You probably need to reinstall MAKER. Using the system perl may be the easiest.

—Carson

https://groups.google.com/g/maker-devel/c/T9NSb8cYjUQ

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于是开始想办法，网上只搜到自己的一篇博客。

开始瞎操作：

思路就是将破碎的Perl修复，然后再更新一次maker。
本服务器的问题是：用conda install maker命令根本就找不到资源。
===================

进入破碎的maker环境：
conda activate maker

perl -MCPAN -e shell

install DBI
install DBD::SQLite
install forks
install forks::shared
install File::Which
install Perl::Unsafe::Signals
install Bit::Vector
install Inline::C
install IO::All
install IO::Prompt

install Bundle::CPAN
install Module::Build
install Bundle::BioPerl # 现在走到这里了，上次这里没有成功【10:03】。
这步卡住：
Please tell me where I can find your apache src
我不知道啊！
#conda install -c conda-forge apache-libcloud # 肯定没用嘛，里面并不包含apache
/etc/httpd 键入这个，有报错提示，不过程序往下运行了。
conda update maker

---

竟然可以直接update。
然而还是没用。

---

---

备用一个方案：
maker 3.01.03 pl5262h8f1cd36_1 anaconda/cloud/bioconda
maker 3.01.03 pl5262h8f1cd36_1 anaconda/cloud/bioconda
maker 3.01.03 pl5262h8f1cd36_1 bioconda
maker 3.01.03 pl5262h8f1cd36_2 anaconda/cloud/bioconda
maker 3.01.03 pl5262h8f1cd36_2 anaconda/cloud/bioconda
maker 3.01.03 pl5262h8f1cd36_2 bioconda
maker 3.01.03 pl526hb8757ab_0 anaconda/cloud/bioconda
maker 3.01.03 pl526hb8757ab_0 anaconda/cloud/bioconda
maker 3.01.03 pl526hb8757ab_0 bioconda

conda update -n base conda
conda create -n maker3
conda activate maker3
conda install perl-bioperl # o..ok

conda install maker=3.01.03 -y -c bioconda

哈哈，并没有意外，装不上。

将之前的maker安装记录拷贝到新的环境里面。
然后运行：
conda update maker

=============================还是不行=================
===脑袋不想装了，反正报错了也能用，但是手还在找方案===
======================================================

下载最新的maker安装包maker-3.01.03-pl5262h8f1cd36_2.tar.bz2

conda install –use-local maker-3.01.03-pl5262h8f1cd36_2.tar.bz2
#安装包
maker -h
-bash: /abysw/app/miniconda3/envs/maker6/bin/maker: /abysw/app/miniconda3/envs/maker6/bin/perl: bad interpreter: No such file or directory
#运行显示没有perl
conda install perl

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conda install -c bioconda/label/cf201901 maker # 安装成功
==========================================================
应该没有后续了。

$ conda create - n maker3 - c bioconda / label / cf201901 maker

========================================================

conda create -n maker3
conda activate maker3
conda install perl-bioperl -y
conda install -c bioconda/label/cf201901 maker

=================再有问题就是网络的问题了===============

$ conda install -c bioconda/label/main maker=3.01.03 -y